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I-TASSER results for job id Rv1889c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)
 Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.10 4 1xvgA BRJ Rep, Mult 19,22,23,26,83,87
20.08 3 4tt0B IOD Rep, Mult 85,86,89
30.08 3 3fu1A ZN Rep, Mult 87,91
40.05 2 1qghA FE Rep, Mult 91,95
50.05 2 1smyF MG Rep, Mult 26,83,86
60.05 2 1xvgA BRJ Rep, Mult 36,37,38,84,87,88
70.03 1 2uyqA SAM Rep, Mult 23,25,43,44,45,47
80.03 1 2uyqA SAM Rep, Mult 109,111
90.03 1 5sy7B NUC Rep, Mult 78,86

Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0601qdbA0.4794.440.0170.7631.7.2.2NA
20.0601khoA0.3934.110.0220.6103.1.4.3NA
30.0601r5zA0.4845.020.1040.9243.6.3.1494,96
40.0601f8iA0.4914.250.0440.7974.1.3.186
50.0602drsA0.4664.590.0580.8643.2.1.156112
60.0603gayA0.4604.210.0190.7464.1.2.13NA
70.0601clcA0.4904.570.1060.8733.2.1.4NA
80.0602yyjA0.4714.440.0350.7461.14.13.321
90.0601og2A0.4394.610.0430.7711.14.14.1NA
100.0603bkkA0.4914.300.0340.8143.4.15.1NA
110.0601mhyD0.4984.190.1000.7971.14.13.2587
120.0601ei1A0.4684.830.0520.8565.99.1.3NA
130.0601fziA0.5123.910.0620.7711.14.13.2587
140.0601ia7A0.5314.610.0440.9243.2.1.4NA
150.0602jbmA0.4703.220.1120.6612.4.2.1991
160.0601ca1A0.4694.100.0740.6863.1.4.3NA
170.0603bnjA0.4474.350.0440.7291.7.2.2NA
180.0601rsrB0.4863.780.0530.7371.17.4.182
190.0601j38A0.4734.420.0930.7463.4.15.1NA

(a)CscoreEC is the confidence score for the EC number prediction. CscoreEC values range in between [0-1];
where a higher score indicates a more reliable EC number prediction.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided
by length of the query protein.

  Gene Ontology (GO) terms

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.510.7600.950.460.802uyoA GO:0008168 GO:0016740 GO:0032259
10.210.8940.870.440.932ckdA GO:0008168 GO:0016740 GO:0032259
20.080.6112.540.160.791rjdC GO:0005829 GO:0006481 GO:0008168 GO:0010506 GO:0016740 GO:0018423 GO:0032259 GO:0043623
30.070.4963.410.080.721rjgA GO:0005829 GO:0006481 GO:0008168 GO:0010506 GO:0016740 GO:0018423 GO:0032259 GO:0043623
40.070.5902.150.170.703p71T GO:0003880 GO:0005829 GO:0006464 GO:0006479 GO:0006481 GO:0008168 GO:0008276 GO:0008757 GO:0010906 GO:0016740 GO:0018423 GO:0031333 GO:0032259 GO:0042981 GO:0090266
50.070.4483.260.180.663o7wA GO:0003880 GO:0005829 GO:0006464 GO:0006479 GO:0006481 GO:0008168 GO:0008276 GO:0008757 GO:0010906 GO:0016740 GO:0018423 GO:0031333 GO:0032259 GO:0042981 GO:0090266
60.070.5513.590.040.852zwaB GO:0005737 GO:0005739 GO:0005829 GO:0006400 GO:0008033 GO:0008168 GO:0008175 GO:0008757 GO:0016740 GO:0030488 GO:0031591 GO:0032259
70.060.3945.040.050.723tiiB GO:0000166 GO:0006464 GO:0046872
80.060.3095.140.060.613fdsA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
90.060.3224.750.060.604k2dA GO:0015035 GO:0042597 GO:0045454 GO:0055114
100.060.3274.950.060.594mkiA GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016787 GO:0016887 GO:0043190
110.060.3215.200.030.654f4wA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
120.060.3264.700.020.614dcmA GO:0003676 GO:0005737 GO:0006364 GO:0008168 GO:0008990 GO:0016740 GO:0031167 GO:0032259 GO:0052916 GO:0070475
130.060.3684.340.110.633ggdA
140.060.3185.390.040.663jwhA GO:0001510 GO:0008171 GO:0008173
150.060.3334.680.000.573lyhB GO:0009236 GO:0016852
160.060.3244.000.040.501q6aA GO:0006468 GO:0007623 GO:0042802 GO:0048511
170.060.2635.290.040.533kvtA GO:0005216 GO:0005244 GO:0005249 GO:0005267 GO:0006810 GO:0006811 GO:0006813 GO:0008076 GO:0016020 GO:0016021 GO:0034765 GO:0046872 GO:0051260 GO:0055085 GO:0071805
180.060.2674.890.040.493ougA GO:0004068 GO:0005737 GO:0006523 GO:0015940 GO:0016829 GO:0016831


Consensus prediction of GO terms
 
Molecular Function GO:0003880 GO:0008757
GO-Score 0.39 0.39
Biological Processes GO:0018410 GO:0006479
GO-Score 0.39 0.39
Cellular Component GO:0044444
GO-Score 0.39

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.